Method of reconstituting cellular spectra useful for detecting cellular disorders

ABSTRACT

Embodiments of the present disclosure provides improved methods for determining the presence of abnormalities in exfoliated cells. In one embodiment, the present disclosure provides methods for reconstructing cellular spectrum of a cell sample by creating a spectral map of the cellular sample, generating a binary mask of the spectral map, removing edge artifacts from each cell, and co-adding spectral data of each pixel corresponding to the cell to reconstruct the spectrum of each cell.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application claims priority to provisional U.S. Application Ser.No. 61/056,955, filed on May 29, 2008, which is herein incorporated byreference in its entirety.

FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT

This invention was sponsored by National Cancer Institute of the NIH(Grant # CA 090346), and thus the U.S. government has certain rights inthis application.

FIELD OF THE INVENTION

The present disclosure generally relates to spectral characterization ofcells, and diagnosis of disease. More particularly, the disclosurerelates to methods for reconstructing spectra of cells from data setscollected by spectral mapping or imaging. Such reconstructed spectra maybe used for determining the distribution and location of normal andabnormal cells in a cell sample disposed on a substrate, and thus fordiagnosing a benign disorder, a viral infection, a pre-disease ordisease state.

BACKGROUND OF THE INVENTION

A number of diseases are presently diagnosed using classicalcytopathology methods involving examination of nuclear and cellularmorphology and staining patterns. Typically, this occurs by theexamination of up to 10,000 cells in a sample and the finding of about10 to about 50 cells that are abnormal. This finding is based onsubjective interpretation of visual microscopic inspection of the cellsin the sample.

An example of this diagnostic methodology is the Papanicolaou smear (Papsmear). Monitoring the onset of cervical disease by detectingpremalignant and malignant cells using the Pap smear has greatly reducedthe mortality rate due to cervical cancer. Nevertheless, the process ofscreening Pap smears is labor intensive and has changed little since itwas first described by Papanicolaou almost 50 years ago. To perform thetest, endo- and ectocervical exfoliated cells from a patient's cervixare first scraped using a brush and spatula or a cytology broom. Becausecervical disease often originates from the cervical transformation zone,i.e., the border between the endocervix (covered by glandular orcolumnar epithelial cells) and the ectocervix (covered by stratifiedsquamous epithelial cells), cells from this area are sampled by theexfoliation procedure. The scraping is then smeared, or otherwisedeposited, on a slide, and the slide is stained with hematoxylin/eosin(H&E) or a “Pap stain” (which consists of H&E and several othercounterstains), and microscopically examined. The microscopicexamination is a tedious process, and requires a cytotechnologist tovisually scrutinize all the fields within a slide to detect the oftenfew aberrant cells in a specimen. This process can be analogized tolooking for needles in haystacks where most haystacks contain few if anyneedles. Consequently, the detection of abnormal specimens depends onthe level of a cytotechnologist's experience, quality of the smearpreparation, and the work load. As a result of these concerns, attemptshave been made both to automate the Pap screening process, and developother objective alternatives. Recent developments in classical cytologyhave focused on preparing better cell deposits, eliminating clumps ofcells, and confounding materials such as mucus, erythrocytes etc.

Other techniques focus on improving the diagnostic step, which relies onvisual inspection by the cytologist. Automated image analysis systemshave been introduced to aid cytologists in the visual inspection ofcells. These methods aid in selecting cells that need further humaninspection by eliminating the most “normal” cells from the cellpopulation. However, these techniques are expensive, labor intensive,and do not aid in all desirable cell diagnoses.

Consequently, a need exists for improvements in diagnostic techniques.In particular, there remains a need for an improved system and methodfor data acquisition, inspection, and comparison of cytological cellulardata.

SUMMARY

The present disclosure provides, in part, improved methods fordetermining the presence of abnormalities in cells long before suchabnormalities can be diagnosed using classical cytopathological methods.Aspects of the present disclosure provide methods for reconstructing thespectrum of a cell sample by creating a spectral map/spectral image ofthe cellular sample, identifying pixels that correspond to a particularcell, co-adding spectral data of pixels corresponding to that cell toreconstruct the spectrum of that cell, and similarly reconstructing thespectral data of other cells in the sample. Improved methods for theearly detection of disease use the underlying methodology.

In one aspect, the disclosure provides a method of generating a spectrumof a cell. The method comprises (a) receiving a plurality of spectralpixels, each of the spectral pixels corresponding to a portion of thecell, each of the spectral pixels being associated with a plurality ofmeasurements, each of the measurements being associated with anintensity of light at a particular wavenumber, one of the measurementsassociated with each spectral pixel being a sorting measurement, thesorting measurement being associated with a wavenumber within a band ofwavenumbers; (b) identifying a subset of the plurality of the spectralpixels, a first pixel being in the subset, the sorting measurement ofthe first pixel being greater than or equal to the sorting measurementsof the other spectral pixels, other pixels in the plurality of spectralpixels being in the subset if they satisfy a first criteria, a spectralpixel satisfying the first criteria if that spectral pixel's sortingmeasurement is greater than a first threshold; and then (c) generatingthe spectrum, the spectrum having a plurality of reconstructedmeasurements, each of the reconstructed measurements corresponding to aparticular wavenumber, each of the reconstructed measurements beingformed according to a sum of the measurements associated with aparticular wavenumber of all the pixels in the subset.

In some embodiments, the first threshold is a preselected percentage ofthe first pixel's sorting measurement. In certain embodiments, the bandof wavenumbers has a lower end and an upper end, the lower and upperends being user selectable values. In particular embodiments, the lowerend is 1640 cm⁻¹ and the upper end is 1670 cm⁻¹.

In some embodiments, the sorting measurement for each spectral pixel isa peak value of that spectral pixel's associated measurements, the peakvalue being a peak that is closest to a user selectable wavenumber. Inparticular embodiments, the user selectable wavenumber is 1650 cm⁻¹. Incertain embodiments, pixels in the plurality of spectral pixels are inthe subset only if they satisfy both the first criteria and a secondcriteria, a pixel satisfying the second criteria if a difference betweenthe wavenumber associated with the second pixel's sorting measurementand the wavenumber associated with the first pixel's sorting measurementis less than a second threshold. In some embodiments, the secondthreshold is a user selectable number. In certain embodiments, the userselectable number is 4 cm⁻¹.

In some embodiments, the measurements associated with each spectralpixel represent values derived from light intensity measurements.

In another aspect, the disclosure provides a method of analyzing thephysiological state of a test cell. The method comprises (a) generatinga spectrum of the test cell, as described in the aspect and embodimentsabove, and then (b) determining whether the reconstructed spectrum ofthe test call has a predetermined criterion, the predetermined criterionbeing indicative of the physiological state of the test cell.

In some embodiments, the predetermined criterion is generated fromabnormal control epithelial cell spectra or from normal controlepithelial cell spectra.

In certain embodiments, the epithelial cells in the test and controlsamples are endothelial, mesothelial, or urothelial cells.

The disclosure also presents a method of detecting an epithelial celldisorder in a test cell. The method comprises (a) generating a spectrumof a test cell, as described in the previous aspects, and then (b)determining whether the generated spectrum of the test call has apredetermined criterion, the predetermined criterion being indicative ofthe presence of a disorder in the test cell.

In some embodiments, the predetermined criterion is generated fromabnormal control epithelial cell spectra. In certain embodiments, theepithelial cells in the test and control samples are endothelial,mesothelial or urothelial cells. The epithelial cell disorder may be abenign disorder, a viral disorder, or cancer in certain embodiments.

In yet another aspect, the disclosure provides a method analyzing a cellin a sample. The method comprises (a) generating a spectral imagecomprising a plurality of spectral pixels, each spectral pixelcorresponding to a portion of the sample, each spectral pixel beingassociated with a plurality of intensity measurements, each intensitymeasurement representing an intensity of light at a particularwavenumber, one of the intensity measurements associated with eachspectral pixel being an amide I measurement; (b) identifying a subset ofthe spectral pixels, one member of the subset being a max spectralpixel, the max spectral pixel being a spectral pixel corresponding to acell and having an amide I measurement that is greater than or equal tothe amide I measurement of other spectral pixels corresponding to thecell, another member of the subset being a first spectral pixel thatsatisfies a first criteria, a second criteria, and a third criteria, thefirst criteria being that the first spectral pixel corresponds to thecell, the second criteria being that the amide I intensity of the firstspectral pixel is greater than a first threshold, the third criteriabeing that a difference between the wavenumber associated with the firstspectral pixel's amide I measurement and the wavenumber associated withthe max spectral pixel's amide I measurement is less than a secondthreshold; and (c) forming a reconstructed cellular spectrum, thereconstructed cellular spectrum having a plurality of reconstructedintensities, each of the reconstructed intensities corresponding to aparticular wavenumber, each of the reconstructed intensities beingformed according to a sum of the intensity measurements at a particularwavenumber of the pixels in the subset.

BRIEF DESCRIPTION OF DRAWINGS

The following figures are presented for the purpose of illustrationonly, and are not intended to be limiting.

FIG. 1 is a flow diagram for an exemplary method for determiningabnormalities in a cell sample in accordance with one aspect of thedisclosure.

FIG. 2 is a flow diagram for an exemplary method for reconstructingcellular spectral data from pixel level spectral data in accordance withone aspect of the disclosure.

FIG. 2A is a flow diagram for an alternate method for reconstructingcellular spectral data from pixel level spectral data in accordance withan aspect of the disclosure.

FIG. 3 is a schematic diagram of the instrumentation used for theobservation of infrared spectra of cells.

FIG. 4A shows a visual image of small section of cellular sample andcontaining squamous cells.

FIG. 4B shows an infrared spectral map of the cellular sample shown inFIG. 4A collected at 6.25 μm aperture.

FIG. 4C shows a binary map created from the infrared spectral map shownin FIG. 4B.

FIG. 4D shows a comparison of spectra collected via a “single point”approach and the spectra obtained from a method in accordance with anembodiment of the present disclosure.

FIG. 4E shows a comparison of an exemplary pixel spectra contaminated bydispersion artifact (bottom) with a corrected spectrum (top).

FIG. 5 shows a “Scores plot” of normal oral mucosa cells (triangles) andherpes simplex-infected oral mucosa cells (crosses).

FIG. 6 shows a “Scores plot” of cervical cells from two samplesdiagnosed as CIN II/CIN III.

FIG. 7 illustrates the manner in which Principal Component Analysis(PCA) is used to analyze reconstructed cell spectra.

FIG. 8 shows photographs of cells that all appear to be normal based ontheir morphology, some of which are abnormal and detected to be so bymethods disclosed herein. FIG. 8 also shows cellular spectra for thephotographed cells. The spectra were reconstructed using the methoddisclosed herein.

FIG. 9 illustrates calculation of the second and third principlecomponents PC2 and PC3 of a principle component analysis for an exampleset of data.

FIG. 10 illustrates discrimination between different cell types usingreconstructed cellular spectra.

FIG. 11 illustrates another example of discrimination between differentcell types using reconstructed cellular spectra.

DETAILED DESCRIPTION

Unless otherwise defined, all technical and scientific terms used hereinhave the same meaning as commonly understood by one of ordinary skill inthe art to which this disclosure belongs. Although methods and materialssimilar or equivalent to those described herein can be used in thepractice or testing of the present disclosure, suitable methods andmaterials are described below. All publications, patent applications,patents, and other references mentioned herein are incorporated byreference in their entirety. In case of conflict, the presentspecification, including definitions, will control. In addition, thematerials, methods, and examples are illustrative only and not intendedto be limiting.

Improved methods of detecting abnormalities in cells are disclosedherein. As an example, the disclosed methods can detect abnormalities incells that appear entirely normal under a traditional morphologicalanalyses. Such cells if left untreated eventually develop morphologicalcharacteristics indicative of abnormality. The disclosed detectionmethods provide for much earlier detection of such abnormal cells, i.e.,the cells can be detected as abnormal before such morphological changesoccur. The detection of abnormality provided by the disclosed methods isalso more reliable than that of traditional morphologically basedmethods.

One problem with morphologically based detection methods is that changesin cellular morphology characteristic of progressive disease are simplydelayed responses to compositional disturbance of the disease. That is,cellular morphological changes are not the cause of disease; rather,they are a delayed reaction to the disease. Rather than detecting thesedelayed reactions to disease, the disclosed methods can detect cellularabnormalities before such delayed reactions even occur. Thus, thedisclosed methods provide an early and reliable detection of cellularabnormalities.

Another problem with morphologically based detection methods is thatthey typically must be performed on stained cells. The stain makesmorphological features more easily detectable by human observers.However, the presence of the stain also masks cellular characteristicsthat may themselves indicate abnormality. The disclosed methods can beperformed on unstained cells. Thus, the disclosed methods are able touse more information that is directly representative of the cell in thedetection of abnormalities.

The present disclosure provides diagnosis of cellular abnormalitiespotentially leading to disease by monitoring the biochemical changesassociated with the disease that occur before morphological changes canbe detected. These biochemical changes can be detected in all cells froma sample that later takes part in manifestations of disease. This novelmethodology is based on reproducible physical measurements, mathematicalalgorithms, and associated changes in cellular mechanisms.

The present methodology, called Spectral Cytopathology, is a moresensitive and more reproducible technique for screening for disease incell samples than is currently available and can be used to detect theprogression of disease earlier than can classical cytopathology.

As used throughout the disclosure, the term “Spectral Cyto-Pathology”(SCP), unless otherwise indicated, shall mean the method of using amicro-spectrometer to obtain mid-infrared spectral data of multiplecells individually and to analyze the resulting spectra for determiningthe composition changes of the cells during the transition from a normalto a benign disorder, a virally infected or a pre-cancerous or cancerousstate.

The term “test cell” refers to a cell sampled from in vivo or in vitrosources that is being analyzed or observed.

The term “abnormal” refers to cells that have a disorder which mayresult in a benign disorder, a viral disease, or cancer. Abnormal cellshave spectra and criteria determined from spectra that are detectibledifferent than “normal” cells. These abnormal cells may lookmorphologically normal or undiseased, but have the propensity ofdeveloping disorders. “Normal” cells do not have a disorder and can beused as controls. Normal cells can be sampled from subjects that do nothave or that do not develop a disorder.

The term “exfoliated cells” refers to those cells scuffed off, removed,detached, or shed from a tissue surface by natural processes or byphysical manipulation. Exemplary methods of collecting exfoliated cellsinclude, but are not limited to, oral or bladder scraping (using acervical spatula or brush), gynecological exam, filtration from urine,and the like.

The term “epithelial cell” encompasses all cells lining an organincluding, but not limited to, endothelial cells, mesothelial cells, andurothelial cells, that may be squamous, columnar, or cuboidal.

The terms “squamous” “columnar,” and “cuboidal” refer to types ofepithelial cells that are simple or stratified, keratinized orunkeratinized, and/or ciliated or unciliated.

“Simple” squamous cells can be found lining blood vessels, lymphvessels, the mesothelium of body cavities, and the ascending thin limbof the kidney. “Stratified” squamous cells are found lining the hardpalate, the dorsum of the tongue, the gingival, the esophagus, rectum,anus, skin, cervix, vagina, labia majora, orpaharynx, cornea, and theexternal urethra orifice.

“Simple” columnar cells can be found in the ducts on the submandibularglands, attached gingiva, ductuli, epididymis, vas deferens, seminalvesicle, larynx, trachea, nose, membranous urethra, penile urethra, thestomach, small and large intestine, rectum, gallbladder, ductal andlobular epithelium, fallopian tubes, uterus, endometrium, cervix,ejaculatory duct, bulbourethral glands, and prostrate. “Stratifiedcolumnar epithelial cells can be found in the ducts of the submandiburglands attached gingival, ductuli epididymis, vas deferens, seminalvesicle, larynx, trachea, nose, membranus urethra, and penile urethra.

“Simple” cuboidal cells can be found in thyroid follicles, ependyma, theovaries, tubuli recti, rete testis, respiratory bronchioles, and theproximal and distal convoluted tubules of the kidney. “Stratified”cuboidal cells can be found in the sweat gland ducts.

The “physiological state” of cell refers to its general health, i.e.,whether it is normal or abnormal, and to its propensity to developabnormalities including morphological, biochemical, genetic, or otherabnormalities, which can lead to cellular disorders.

A “predetermined criterion” is a value characteristic of normal cells orof abnormal cells.

FIG. 1 delineates a method for detecting abnormalities in a cytologicalcell sample. At step 102, cellular samples are collected and depositedon slides. The cellular samples can include, for example, exfoliatedcells (e.g., endo- and ectocervical cells) collected from the cervicaltransformation zone, i.e., the border between the endocervix (covered byglandular or columnar epithelial cells) and the ectocervix (covered bystratified squamous epithelial cells). Liquid-based methods may be usedto deposit cellular samples on a slide to provide evenly spaced andsparse deposits of cells, eliminate cellular debris and confoundingcells, and maintain acceptable levels of cell population in a givenfield of view. Exemplary liquid-based methods for depositing cellularsamples include, but are not limited to, cyto-centrifugation, theThinPrep® method, the Surepath® methods, and the like. Exemplary slidesfor depositing cellular samples include, but are not limited to,infrared-reflective microscope slides (e.g., “Low-e”® slides).

At step 104, cellular samples deposited on slides are scanned to collectspectral data. For example, infrared spectral data of cellular samplescan be collected using an infrared scanning device (e.g. infraredmicro-spectrometer) at a preset aperture. The area over which data iscollected is divided into pixels, and spectral data is collected at eachpixel. For example, the spectral data of cellular samples can becollected from the entire sample area at a pixel size of about 6.25μm×6.25 μm. The spectra data may include intensity values over a rangeof wavenumber values. The term “intensity” is used herein in accordancewith its broad ordinary meaning, which includes measurements ofabsorbance, transmission, reflective absorbance intensity(transflectance), and the like. At step 106, the collected spectral dataof the cellular sample at each pixel is stored. At step 108, thespectrum of each cell is reconstructed by associating pixels with cellsand co-adding the spectral data of pixels corresponding to a particularcell. Step 108 is described in detail below. Step 110 then determinesthe coordinates of cells in the sample area. At step 112, the cells arestained with at least one staining agent. Exemplary staining agentsinclude, but are not limited to, hematoxylin/eosin (H&E), “Pap stain” (amixture of H&E and other counterstains), and the like. At step 114,visual microscopic images (“photomicrographs”) of all cells are acquiredat coordinates determined in step 110. The images of all cells arestored at step 116. At step 118, scanned images from step 114 andreconstructed cellular spectrum from step 108 are correlated. Thiscorrelation step is used in the training phases of the algorithm, andtypically consists of a cytologist or cyto-technician rendering adiagnosis of the cellular image. This diagnosis will be used toestablish the correlation between classical cyto-pathology and thespectral results. The algorithm may use unsupervised multivariatestatistics to investigate whether the dataset contains quantifiabledifferences or supervised discriminant algorithms that can classifycells based on the spectral data and correlations from standardcyto-pathology or cell biology, or supervised methods trained with cellsof known cyto-pathology.

FIG. 3 shows an example apparatus for measuring the infraredmicro-spectra. Light emitted form an infrared source, generally ametallic or non-metallic solid heated electrically to between 1300° C.and 2000° C., is modulated by an interferometer before being focusedonto the sample by an infrared objective. In this example, the infraredlight passes through the sample, is reflected by the silver layer of the“low-e” slide, passes through the sample again, and is detected andconverted to an electric signal by a suitable infrared detector. Thismethod of measuring infrared spectra by a double passtransmission/reflection is referred to as “transflection.” The ratio ofincident to “transflected” light intensity is converted to “opticaldensity” or “absorbance” units, and is henceforth referred to as“absorbance,” “absorption intensity” or simply as “intensity.”

FIG. 2, generally at 200, illustrates an exemplary method forreconstructing cellular data from spectral data measured at individualpixels. That is, FIG. 2 shows in detail how step 108 shown in FIG. 1 canbe performed. At step 202, infrared spectral data of the cellular sampleare collected from the entire sample area on the microscope slidesmeasuring, e.g., 4 mm×4 mm, at a pixel size of about 6.25 μm×6.25 μm (orany other pixel size significantly smaller than the size of the cells tobe investigated), to generate a dataset consisting of about 409,600pixels with each pixel including about 1600 data points, or colorpoints. Or, infrared spectral data can be collected by mapping orimaging the vicinity of a cell, where the cell's position has beendetermined previously by means other than the binary mask describedabove. That is, each pixel contains many sample intensity measurements,each intensity being measured at a particular wavelength. For example,the intensity measurements may be made in the wavelength range of11.1-5.5 μm, corresponding to a wavenumber range of 900-1800 cm⁻¹, wherethe wavenumber is the inverse of the wavelength and describes the numberof light waves per unit length. The terms “wavenumber” and “frequency”are used interchangeably herein. Step 204 is a step to correct spectraloffset. At step 204, on a pixel-by-pixel basis, the lowest intensityvalue of each pixel's spectrum is subtracted from each intensity valuein the same pixel's spectrum to remove any intensity offset and toensure that all spectra have positive intensity values. For example, atstep 202 a pixel P can include the set of measurements (I₁, I₂, . . . ,I_(N)), where each measurement I_(n) represents an intensity at aparticular wavenumber. If I_(j) is the lowest of these N values, thenafter step 204 the pixel P will have the values (I₁-I_(j), I₂-I_(j), . .. , I_(N)-I_(j)). This normalization step is performed for each pixel.

At step 206, a spectral map of the entire sampling area is created usingthe subtracted spectral data generated at step 204. The number of pixelsin the spectral map created at step 206 is based on the sample areascanned at the predefined pixel size. The spectral map is created byassigning a gray-scale value to each pixel. This grayscale value can bebased on the integrated area of the “amide I” band, which occurs betweenwavenumbers ca. (“approximately”) 1640 and 1670 cm⁻¹ in the infraredspectra of all proteins. The integrated area of the amide I band for apixel P can be calculated, for example, as

${\sum\limits_{j = x}^{y}I_{j}},$

where each I_(j) represents an intensity of the pixel measured atwavenumber j and all intensities measured at wavenumbers between ca.1640 and 1670 cm⁻¹ lie within the range from x to y. Pixels with highintegrated intensities in the amide I band can be assigned a white orlight gray shades, and pixels with the lowest intensities can beassigned black or dark grey shades. The pixels with intensities inbetween the highest and lowest intensity values can be linearly mappedonto the grayscale scale between black and white. FIG. 4B shows a greyscale version of a spectral map obtained from a subset of data from anoriginal dataset of 409,600 pixels. It will be appreciated that thespectral map can also be generated as a color image instead of as agrayscale. FIG. 4A shows a visual image corresponding to the spectralmap of FIG. 4B. The grayscale value can also be based on, for example,the intensity of any band in the spectral region, the ratio between twointensity points in the spectral region, the integrated area between twointensity points in the spectral region or the ratio of the integratedarea between two spectral regions.

The manner in which the amide I intensity of a pixel is determined willnow be discussed. As shown in FIGS. 4D and 4E, the spectrum of a pixelin a cell measured from wavenumbers 900-1800 cm⁻¹ generally includespeaks corresponding to various components of the cell (i.e., due tovibrational excitation of covalently bonded atoms and groups). The peakat about 1650 cm⁻¹ (known as the amide I band) arises from carbonylstretching vibrations of the peptide backbone in cell proteins, and isan indication of the presence of a cell. Thus, the amide I intensity isdetermined by locating the intensity peak that is closest to wavenumber1650 cm⁻¹. The wavenumber at which this peak occurs is referred toherein as (ν_(aI)) and the intensity of that peak is referred to hereinas I_(aI). In other words, if a pixel includes intensity measurements(I₁, I₂, . . . , I_(aI), . . . I_(N)), then I_(aI) is the amide Iintensity, and the wavenumber at which I_(aI) was measured is ν_(aI).

At step 208, a minimum amide I intensity threshold value (I_(aImin)) isset. For example, the minimum amide I intensity threshold value can beset to 0.15 absorbance units in order to reject any pixel that has nowell-defined protein vibrations, and is therefore not due to a cell. Avalue of 0.15 for this threshold corresponds to a situation in which theintensity of the beam received by the detector divided by the intensityof the beam incident on the sample is equal to 0.15. In steps 210-224,the grayscale map created at step 206 is converted to a binary map byusing the threshold (I_(aImin)). Each pixel in the binary mapcorresponds to one pixel in the spectral map produced at step 206, andeach pixel in the binary map is set to one of two values. As illustrated(in FIG. 4C), each pixel in the binary map is set to either white orblack. At step 210, a pixel from the spectral map is selected and theamide I intensity value in the pixel spectra is identified at step 212.That is, if each pixel P, in the spectral map has measurements (I₁, I₂,. . . , I_(N)), and measurement I_(aI) corresponds to the wavenumber ofamide I (ν_(aI)) for that pixel, then I_(aI) is identified in step 212.At step 218, the amide I intensity value identified in step 212, I_(aI),is compared with the minimum amide I intensity threshold value(I_(aImin)) set at step 208. If the amide I intensity value identifiedin step 212, I_(aI), is greater than or equal to the threshold set atstep 208, then at step 220, the corresponding pixel in the binary map isassigned white color. If the amide I intensity value identified in step212, I_(aI), is less than the threshold set at step 208, then at step216, the corresponding pixel in the binary map is assigned black color.Step 222 determines whether the current pixel is the last pixel in thespectral map. If the current pixel is not the last pixel in the spectralmap, then at step 214 next pixel in the spectral map is selected. Steps212 through 222 are repeated until all pixels in the spectral map havebeen selected.

If the current pixel is the last pixel in the spectral map, then at step224, contiguous white areas in the binary map are identified andassociated with a cell or clump of cells. Next, an initial number ofcells in the binary map is identified at step 226 based on the groups ofcontiguous white areas (i.e., the number of contiguous white areas iscounted). The number of pixels in each cell (i.e., each contiguous whitegroup) is counted at step 228, and at step 230, position coordinates ofeach pixel are stored.

Steps 232 through 244 refine the binary map by removing pixelsassociated with clumps of cells, and/or contaminants. At step 232, upperand lower limits for the number of pixels contributing to each singlecell are set. For example, upper and lower limits for the number ofpixels contributing to one cell can be set in order to remove from thebinary map pixels contributing to overlapping squamous cells measuringmore than about 60 μm across. As an example, an upper limit of 90 pixelsprevents contiguous white pixels in the binary map that correspond tolarge mature squamous cells, or that correspond to large clumps ofoverlapping cells, from being further analyzed. The lower limit for thenumber of pixels defining a cell can be set at about 15 to preventcontiguous white pixels in the binary map that correspond tocontaminants from being further analyzed. Exemplary contaminantsinclude, but are not limited to, erythrocytes (red blood cells, whichmeasure about 6 μm, or 1 pixel, in size), naked nuclei of fragmentedcells, and the like.

At step 234, a single cell (i.e., a single group of contiguous whitepixels) from the cells identified in the binary map is selected. At step238, the number of pixels associated with the cell is compared to theupper and lower pixel limits set at step 232. If the number of pixels inthe selected cell is not within the upper and lower pixel limits, thenat step 236 the selected cell is discarded. If the number of pixels inthe selected cell is within the upper and lower pixel limits, then atstep 240, the selected cell is included for subsequent analysis. A nextcell in the binary map is selected at step 242. At step 244, the methoddetermines whether all cells (i.e., contiguous white groups of pixels)have been compared against the upper and lower limits. If all cells havenot yet been compared, then another cell is selected and compared to thelimits in step 238. If at step 244, all cells have been compared againstthe upper and lower limits, then control moves to step 246.

In other words, steps 234-244 screen out regions of contiguous whitepixel areas in the binary map that are either too big or too small to becells of interest. These steps in effect produce a refined binary map,by discarding the regions that were too big or too small. The resultingbinary map from step 244 delineates the pixels that belong to cells ofinterest in the sample.

FIG. 4C shows an exemplary binary map created from spectral map shown inFIG. 4B, which corresponds to the cellular sample image shown in FIG.4A. The binary map shown in FIG. 4C identifies six cells of interest,each cell corresponding to one of the contiguous groups of white pixels.At step 246, the number of cells in the sample is updated to equal thenumber of cells identified in the refined binary map from step 244.

The spectrum of each cell identified in the binary map is reconstitutedfrom the individual pixel spectra using steps 248 through 262. At step248, a single cell is selected from the cells identified in the refinedbinary map produced at step 244. At step 250, the pixel in the cell thathas the highest amide I intensity value (“I_(aImax)”) is identified. Thepixel with the highest amide I intensity (i.e., the I_(aImax) value)corresponds to the region of the cell with the highest proteinconcentration, normally the nucleus of the cell. Next, a white pixelthat is associated with the same cell and that is adjacent to the pixelselected at step 250 is identified at step 254. The pixel identified atstep 254 may correspond to the perinuclear region of the cell.

At step 256, two criteria (both of which are described below) of theselected pixel are checked. If the pixel meets both criteria, then thespectrum of the selected pixel is co-added to the spectrum of the pixelwith the I_(aImax) value. Two spectra are co-added as follows. If pixeli (p_(i)) contains intensity measurements (I_(pi1), I_(pi2), . . . ,I_(piN)) and pixel n (p_(n)) contains intensity measurements (I_(pn1),I_(pn2), . . . , I_(pnN)), then the co-addition of the spectra frompixels i and n is produced by summing the intensity measurementscomponent-by-component, to produce (I_(pn1)+I_(pi1), I_(pn2)+I_(pi2), .. . , I_(pnN)+I_(piN)). This co-added spectrum is a “reconstructed”spectrum. Steps 252-264 reconstruct the spectrum of a cell by co-addingthe spectra of all pixels in the cell that meet the criteria checksperformed in step 256. Also at step 256, the pixel could be selected by,for example, the intensity of any band in the spectral region, the ratiobetween two intensity points in the spectral region, the integrated areabetween two intensity points in the spectral region or the ratio of theintegrated area between two spectral regions.

The first of the two criteria checks at step 256 is to compare the amideI intensity (i.e., the I_(aI) value) in the pixel selected at step 254with a threshold intensity value to determine whether the amide Iintensity (I_(aI)) is greater than or equal to the threshold intensityvalue. The threshold can be set to a predefined percentage (e.g., 66percent) of the I_(aImax) value (i.e., a percentage of the I_(aI) valueof the pixel in the cell that had the highest amide I intensity, theI_(aImax) value). If the I_(aI) value of the pixel is below thethreshold, then the pixel is discarded (i.e., its spectrum is notco-added to that of other pixels in the cell). This evaluation at step256 eliminates pixel spectra associated with the outer edges of thecytoplasm, which are generally thin, and are associated with weak andnoisy spectra.

If the pixel meets the amide I intensity criteria (i.e., its I_(aI)value is greater than the threshold), then step 256 further determineswhether the pixel is associated with edge artifacts. Exemplary edgeartifacts include, but are not limited to, dispersion artifacts,artifacts caused by reflective and/or absorptive components of thepixel, artifacts caused by inaccurate phase corrections, and the like.At step 256, the wavenumber (i.e, the ν_(aI) value) corresponding toamide I intensity (i.e., the I_(aI) value) in the pixel is compared withthe wavenumber (i.e, the ν_(aImax) value) corresponding to the highestamide I intensity (i.e., the I_(aImax) value) in the cell. If the ν_(aI)value is not equal to the ν_(aImax) value, then the shift in the ν_(aI)value from the ν_(aImax) value (i.e., the Δ(ν_(aImax)−ν_(aI)), thatvalue being equal to the absolute value of (ν_(aImax)−ν_(aI)) isdetermined. Further at step 256, the Δ(ν_(aImax)−ν_(aI)) value iscompared with a threshold amide I wavenumber shift value to determinewhether the Δ(ν_(aImax)−ν_(aI)) value is less than or equal to thethreshold wavenumber shift value. For example, the threshold wavenumbershift value can be set to 4 cm⁻¹.

FIG. 4E shows a comparison of an exemplary pixel spectra contaminated bydispersion artifact (bottom) with an uncontaminated spectrum (top). InFIG. 4E, the amide I wavenumber in the contaminated spectrum is about1610 cm⁻¹ and the amide I wavenumber in the good spectrum is about 1650cm⁻¹. If the amide I wavenumber shift (the Δ(ν_(aImax)−ν_(aI)) value) ofthe pixel is less than or equal to the threshold wavenumber shift value,then at step 258, the spectrum of the pixel is co-added to that of otherpixels in the cell. Otherwise, the pixel is discarded and not co-addedwith other pixels.

At step 262, the method determines whether all pixels in the cell haveeither been discarded or had their spectra co-added to the spectra ofother pixels in the cell. If white pixels in the cell remain that havenot been so discarded or co-added, then control returns to step 256.Otherwise, control proceeds to step 264.

Similarly, at step 264, the method determines whether all cellsidentified in the refined binary map (produced at step 244) have hadtheir spectra reconstructed (by co-addition of spectra of pixels in thecell). If all cells have had their spectra reconstructed, then controlproceeds to step 266. Otherwise, control proceeds to step 252 so anothercell can be selected and the spectra of that cell can be reconstructed.At step 266, the co-added spectrum of each cell is stored along with theposition coordinates of the cell. As an example, the positioncoordinates of a cell can correspond to center of absorbance of thatcell. The cell spectrum can be constructed by co-adding from about 30 toabout 70 individual pixel spectra.

FIG. 4D shows an exemplary cellular spectrum constructed by co-adding 15(out of 36) individual pixel spectra corresponding to a single cellidentified in the binary map shown in FIG. 4B. FIG. 4D also shows acomparison of the cellular spectrum obtained using the method discussedabove (shown in gray) with a single point cellular spectrum (shown inblack) of the same cell obtained using conventional techniques.

FIG. 4D illustrates that the co-addition process described in connectionwith FIG. 2 results in a spectrum (shown in gray) that is almostidentical to the single point cellular spectrum (shown in black). Thatis, the spectrum of a cell produced according to the method described inconnection with FIG. 2 is of similar quality to the spectrum of the samecell produced by conventional techniques. The method described inconnection with FIG. 2 is advantageous, as compared to conventionaltechniques, though at least because the spectra of each pixel can besampled in a regular fashion at a fixed aperture. The loss ofsignal-to-noise ratio in any given pixel, caused by sampling at anaperture that is smaller than a cell, is recovered by the co-additionprocess. That is, the co-addition process results in a gain in SNR by afactor of about 4 to 8. This gain in SNR compensates for the loss insignal quality of individual pixel spectra due to data collection at avery low effective aperture (e.g., 6.25 μm×6.25 μm).

FIG. 2A shows method 200′, which is an alternative to the method 200discussed above for generating the reconstructed spectrum of a cell.Method 200′ shown in FIG. 2A is similar to method 200 of FIG. 2 andemploys many of the same steps. However, instead of steps 206, 208, 212,250, 254, and 256, method 200′ uses steps 206′, 208′, 212′, 250′, 254′,and 256′, respectively. The asterisks in steps 206′, 208′, 212′, 250′,and 254′ mean that the spectra for those steps (e.g., A1 for step 206′)may be in the form of transmittance, absorbance, reflectance, derivativeor interferogram and are generated by any of the following: (a)measuring the intensity at any wavenumber; (b) calculating the ratiobetween two intensity values at any wavenumber; (c) calculating theintegrated area between two intensity values at any wavenumber; or (d)calculating the ratio of an integrated area between two intensity valuesat any wavenumber. In step 206′, the spectral map can be based on anyselected intensity as opposed to just the intensity or the integratedarea of the amide I band as was the case in step 206. Similarly, insteps 208′ and 212′, the minimum threshold A1 can be compared to anyselected value of the pixel as opposed to the amide I intensity value.Also, in step 250′, a pixel can be selected based on having a maximumvalue at any selected wavenumber and the wavenumber corresponding toamide I need not be used. Then in steps 254 and 256, pixels are retainedor discarded based on intensity at a particular wavenumber and again thewavenumber corresponding to amide I need not be used.

A variety of cells can be examined using the present methodology. Suchcells may be exfoliated cells including epithelial cells. Epithelialcells are categorized as squamous epithelial cells (simple orstratified, and keritized, or non-keritized), columnar epithelial cells(simple, stratified, or pseudostratified; and ciliated, or nonciliated),and cuboidal epithelial cells (simple or stratified, ciliated ornonciliated). These epithelial cells line various organs throughout thebody such as the intestines, ovaries, male germinal tissue, therespiratory system, cornea, nose, and kidney. Endothelial cells are atype of epithelial cell that can be found lining the throat, stomach,blood vessels, the lymph system, and the tongue. Mesothelial cells are atype of epithelial cell that can be found lining body cavities.Urothelial cells are a type of epithelial cell that are found lining thebladder. These cell types have been distinguished by the methoddescribed here (summarized in Table 1).

TABLE 1 System Tissue Epithelium Type circulatory blood vessels Simplesquamous digestive ducts of Stratified columnar submandibular glandsdigestive attached gingiva Stratified squamous, keratinized digestivedorsum of tongue Stratified squamous, keratinized digestive hard palateStratified squamous, keratinized digestive oesophagus Stratifiedsquamous, non-keratinised digestive stomach Simple columnar,non-ciliated digestive small intestine Simple columnar, non-ciliateddigestive large intestine Simple columnar, non-ciliated digestive rectumSimple columnar, non-ciliated digestive anus Stratified squamous,non-keratinized superior to Hilton's white line Stratified squamous,keratinized inferior to Hilton's white line endocrine thyroid folliclesSimple cuboidal digestive gallbladder Simple columnar, non-ciliatednervous ependyma Simple cuboidal lymphatic lymph vessel Simple squamousintegumentary skin - dead Stratified squamous, keratinized superficiallayer integumentary mesothelium of Simple squamous body cavities mammaryductal and lobular columnar epithelium reproductive - female ovariesSimple cuboidal reproductive - female Fallopian tubes Simple columnar,ciliated reproductive - female uterus Simple columnar, ciliatedreproductive - female endometrium Simple columnar reproductive - femalecervix Simple columnar (endocervix) reproductive - female cervix(ectocervix) Stratified squamous, non-keratinised reproductive - femalevagina Stratified squamous, non-keratinised reproductive - female labiamajora Stratified squamous, keratinised reproductive - male tubuli rectiSimple cuboidal reproductive - male ductuli efferentes Pseudostratifiedcolumnar reproductive - male epididymis Pseudostratified columnar, withstereocilia reproductive - male vas deferens Pseudostratified columnarreproductive - male ejaculatory duct Simple columnar reproductive - malebulbourethral glands Simple columnar (gland) reproductive - male seminalvesicle Pseudostratified columnar (gland) reproductive - prostatecolumnar male respiratory oropharynx Stratified squamous,non-keratinised respiratory larynx Pseudostratified columnar, ciliatedrespiratory larynx - True vocal Stratified squamous, non-keratinisedcords respiratory trachea Pseudostratified columnar, ciliatedrespiratory respiratory bronchioles Simple cuboidal sensory corneaStratified squamous, non-keratinised sensory nose Pseudostratifiedcolumnar urinary kidney - ascending thin Simple squamous limb urinarykidney - distal Simple cuboidal, non-ciliated convoluted tubule urinarykidney - collecting duct Simple cuboidal urinary renal pelvisTransitional urinary ureter Transitional urinary urinary bladderTransitional urinary prostatic urethra Transitional urinary membranousurethra Pseudostratified columnar, non-ciliated urinary penile urethraPseudostratified columnar, non-ciliated urinary external urethralorifice Stratified squamous

Disorders affecting any of these cells are detectable using themethodology of the present disclosure. For example, this methodologydetects viral infections, such as, but not limited to, Herpes simplex,HPV, and Epstein Barr virus, and disorders such as dysplasia andmalignancy-associated changes indicative of cancer, and changes ofcellular maturation and differentiation that can be indicative of apre-disease state such as benign reactive changes including hyperplasia,metaplasia, and inflammation.

As described in the examples below, several experiments have establishedthe utility of the reconstructed spectra generated according to themethod described above in connection with FIG. 2. For example,reconstructed spectra have been generated for three broad categories ofcells: (a) normal cells collected from normal patients; (b) cells thatappear morphologically normal that were collected from patients known tohave a disorder; and (c) cells that appear morphologically abnormal thatwere collected from patients known to have a disorder. Conventionalmorphological analysis can discriminate between types (a) and (c) (i.e.,cells that appear morphologically normal and cells that appearmorphologically abnormal). However, conventional morphological analysisdoes not discriminate between types (a) and (b) (i.e., normal cells andcells that visually appear normal that were collected from patients withknown disorders). However, as described below, the reconstructed spectraof the type (b) cells (i.e., cells that visually appear normal that werecollected from patients with known disorders) are different than, andcan be discriminated from, the type (a) cells (i.e., normal cells).Methods described below readily and automatically discriminate betweentype (a) cells and type (b) cells thus allowing earlier and morereliable diagnosis than is possible with conventional morphologicaltechniques.

A more complete understanding of the present disclosure can be obtainedby referring to the following illustrative examples of the practice ofthe disclosure, which examples are not intended, however, to undulylimit the disclosure.

EXAMPLES

The following examples illustrate the results obtained from analysis ofcytological samples using the methods of the present disclosure.

Example 1 Spectral Analysis of Oral Mucosal Samples

This example illustrates the analysis of cytological samples of oralmucosa cells, exfoliated from a patient with a Herpes simplex outbreakin the oral cavity, using the methods of the present disclosure. Thecytological samples of oral mucosa cells were obtained from New EnglandMedical Center (NEMC), Boston, Mass. Infrared pixel level spectral dataof these samples were acquired from the entire sample area. Infraredspectra of individual cells in the sample were then reconstructed fromthe sampled area using the technique described above in connection withFIG. 2. Subsequently, the reconstructed cell spectra were analyzed byunsupervised methods of multivariate statistics, in particular, byPrincipal Component Analysis (PCA), to establish whether or not spectraldifferences could be found that are indicative of the disease.

FIG. 7 illustrates the principles of PCA. FIG. 7A illustrates eightsimulated spectra, similar to those which are reconstructed spectra foreach of eight cells. As shown, the eight spectra are all similar, butnot identical. A set of “basis spectra” are then created from thespectra of the cells shown in FIG. 7A. FIG. 7B delineates an example ofthree such basis spectra. The basis spectra are chosen to contain themaximum variance in the original dataset. Subsequently, each of the cellspectra shown in FIG. 7A are reproduced as linear combinations of thebasis spectra. That is, each spectrum S_(j), can be expressed as

${S_{j} \cong {\sum\limits_{n = 1}^{N}{a_{jn}B_{n}}}},$

where B_(n) is the nth basis spectra (there are N basis spectra), anda_(jn) is the nth coefficient for the jth spectra. Since each spectrumcan be expressed as a linear sum of the basis spectra, the basis spectracan be thought of as “principle components” of the spectra. FIG. 7Cillustrates the reconstructed spectra that are formed as linearcombinations of the basis spectra, and as illustrated, the artificiallyreconstructed spectra shown in FIG. 7C are substantially identical tothe original spectra shown in FIG. 7A. The coefficients can then be usedto discriminate between the cells. The basis spectra are generated bycomputing the variances between the original reconstructed spectra(e.g., as shown in FIG. 7A), arranging those variances in a matrix andthen solving for the matrix's eigenvalues. This technique of computingbasis spectra and then resolving original spectra into principlecomponents is well known and is described for example in Adams, M. J.,Chemometrics in Analytical Spectroscopy. 2nd ed.; Royal Society ofChemistry: Cambridge, 2004.

The first basis spectrum is simply the average of all spectra and isgenerally not of much use in discriminating between cells. Also,coefficients for higher order basis spectra tend to be small, ornegligible, and are also generally not of much use in discriminatingbetween cells. However, the coefficients of the 2^(nd), 3^(th), and4^(th) components are often useful for discriminating between cells thathave different characteristics.

The aim of PCA is to reduce a large number of variables down to a smallnumber of summary variables, or principal components (PCs), that explainmost of the variance in the data. All PCs are orthogonal and eachsuccessive component expresses decreasing amounts of variation with mostof the variation explained by the first few components. This enables themulti-dimensional data to be represented in two or three dimensions,which are easily visualized. The technique works by transforming theoriginal variables onto a new set of axes in the direction of thegreatest variation in the data. FIG. 9 shows an example of how thesecond and third principle components, PC2 and PC3 are measured for anexample data set.

Referring to FIG. 9, the second principle component (PC2) is orientedalong the axis of greatest variance of the variables in the data matrixabout their means (i.e., averages). The third principle component (PC3)is independent of (orthogonal to) the second PC and is the vector alongthe axis of next largest variance in the data. Succeeding PCs can becalculated which will be orthogonal to the preceding ones and whichexplain some of the remaining variance. The PCs are linear combinationsof the original variables, which are fitted in the least squares sensethrough the points in measurement space. These new variables usuallyresult in a reduction of variables from the original set and often canbe correlated with physical or chemical factors.

FIG. 5 shows a PCA “Scores Plot” of the analysis for oral mucosa cells.The data set analyzed consisted of ca. 1000 spectra of cells harvestedfrom five healthy volunteers, and ca. 400 spectra of cells collectedfrom a patient with an acute oral herpes simplex lesion. These cellswere harvested directly from the lesion, where the majority of thesecells are likely to be infected by the virus. Visual inspection of thesecells, stained after infrared data acquisition, confirmed that thesecells were infected by the virus.

In FIG. 5, the X axis represents the coefficient of the 2^(nd) principalcomponent and the Y axis represents the coefficient of the 3^(rd)principal component. That is, the spectra of all cells werereconstructed from pixel level spectra according to the method describedin connection with FIG. 2, each of those spectra were then expressed asa linear sum of basis vectors as described in connection with FIG. 7,and then the spectra of each cell was plotted as a single point on FIG.5. The location on FIG. 5 of each point was determined by thecoefficients for the second and third basis spectra for thereconstructed spectra corresponding to that point. In FIG. 5, the normalcells (shown as triangles) form a tight cluster which is well separatedfrom the virus-infected cells (shown as crosses). Thus, FIG. 5 shows howPCA can be used to discriminate between cells with differentcharacteristics, in this case normal cells from virus-infected cells. Itshould be noted that the method for analyzing the spectra, PCA, is by nomeans an increased diagnostic algorithm, but simply a procedure thatestablished whether or not there are quantifiable differences betweengroups of spectra. Thus, this result presents proof-of-concept that themethods in accordance with an embodiment of the present disclosure candistinguish spectral patterns due to a viral infection.

Example 2 Spectral Analysis of Cervical Sample

This example illustrates the analysis of cervical samples diagnosed withlow grade/high grade squamous intraepithelial lesions (LGSIL/HGSIL)using the methods of the present disclosure. The cervical samples wereobtained from NEMC, and were from women whose standard cytopathologicaldiagnoses were CIN II/CIN III (CIN diagnoses represent tissue diagnosticgrades of cervical intraepithelial neoplasia, grades I to III). Thesesamples were collected using gynecological brushes that were deliveredto the inventors in standard fixation solution. Cervical dysplasia is adisease that starts in small foci, typically between 0.5 to a fewmillimeter in size. Thus, sampling of the entire cervical area (severalsquare centimeters in size) generally includes a majority of normalcells mixed with a few abnormal cells. The degree of disease in thesecells may vary from very mild atypia to more serious SIL, or evencarcinoma in situ. As with Example 1, infrared pixel level spectral dataof these samples were acquired from the entire sample area. The infraredspectral data were processed using the methods in accordance with anembodiment of the present disclosure to construct cellular spectra fromthe individual pixel spectra as described in connection with FIG. 2.Subsequently, the cell spectra were analyzed by unsupervised methods ofmultivariate statistics, in particular, by Principal Component Analysis(PCA), as described in connection with FIG. 7, to establish whether ornot spectral differences could be found that are indicative of disease.

FIG. 6 illustrates that early stages of cervical cancer can be detectedby infrared spectral methods in accordance with an embodiment of thepresent disclosure. Analysis of normal cells by infrared spectroscopyand PCA generally show a near-spherical distribution in the scores plot.The cells in FIG. 6, whose scores along the PC 2 (i.e., second principalcomponent) axis fall in the range of between 0.3 to 0.8, fall outsidethe near-spherical distribution of the normal cells, and upon visualinspection, show morphologies consistent with dysplasia. These resultsdemonstrate that infrared spectral discrimination of abnormal cells inexfoliated samples of cervical cells is possible. Furthermore, thesedata suggest that a quantitative scale of spectral diagnosis can beestablished.

Example 3

Reconstructed Spectra Versus Morphology

FIG. 8 shows photographs of three cells. Panel A shows a photograph of anormal cell. Panel B shows a cell that appears normal based on itsmorphology but in fact has cellular spectra indicative of LSIL/HSIL.Panel C shows a cell that appears normal based on its morphology but infact has cellular spectra indicative of HSIL.

FIG. 8 thus illustrates the usefulness of the method shown in FIG. 2 forreconstructing cellular spectra. All of the cells shown in FIG. 8 appearnormal based on their morphology. Thus, a conventional morphologicalexamination (e.g., a PAP examination) of the cells shown in FIG. 8 wouldlikely result in a diagnosis of “normal.” However, the reconstructedcellular spectra for the cells shown in FIG. 8, produced according tothe method described above in connection with FIG. 2, indicate that thecells in Panels B and C are abnormal. Had these cells been allowed tocontinue to grow, it is believed that they would have eventuallydeveloped the morphological features typically indicative of LSIL/HSILand HSIL.

The reconstructed cellular spectra for the cells shown in panels A-C areshown in FIGS. 8D-8F, respectively. As shown, the reconstructed spectrafor the normal and abnormal cells appear similar, but they in factcontain differences that allow the normal cells to be discriminated fromthe abnormal cells. For example, the automated principle componentanalysis disclosed herein distinguishes the normal cells from theabnormal cells.

Example 4 Sample Preparation

Clinical oral samples were obtained in collaboration with the PathologyDepartment at Tufts Medical Center (Boston, Mass. USA) after routinetesting and follow-up had been performed. Samples (on cytologicalbrushes) were stored in SurePath® solution (Burlington, N.C. USA).Subsequently, cells were vortexed free of the brushes, filtered toremove debris, and deposited onto reflective substrates (“low-e” slides,Kevley Technologies, Chesterland, Ohio USA) using cytocentrifugation(CytoSpin, Thermo, Waltham, Mass. USA).

Normal oral cytology samples were collected from healthy laboratoryvolunteers at Northeastern University under a local IRB. Theseexfoliations of normal oral cavity cells were obtained from five regionsof the mouth, to correlate specific spectral changes contributed byorigin of the oral cavity. Samples were taken from the cheeks, tongue,hard palate, gums, and floor of the mouth. Before sampling, the subjectspre-rinsed their mouth with water to generally rid the cavity of anydebris. Subsequently, oral mucosa cells were obtained by 30 secondswabbing of the area of interest using a Fisherbrand sterilizedpolyester swab. In drug metabolite experiments, oral mucosa cells werecollected in similar fashion, one hour after ingestion of 600 mg ofIbuprofen. All cells were immediately fixated in SurePath® fixativesolution and prepared onto low-e slides in a similar fashion asdescribed above for the clinical samples.

Data Collection

The unstained slides were interrogated by a beam of IR light thatanalyzes pixels of 6.25×6.25 μm² in size, from a 4.0×4.0 mm² sample spotusing a PerkinElmer Spotlight 400 FTIR Imaging System, (Perkin Elmer,Shelton, Conn. USA). The instrument optical bench, the infraredmicroscope and an external microscope enclosure box were purged with acontinuous stream of dry air (−40° C. dew point) to reduce atmosphericwater vapor spectral contributions. Data were acquired using thefollowing parameters: 4 cm⁻¹ spectral resolution, Norton-Beerapodization, 1 level of zero-filling, and no atmospheric backgroundcorrection. Two co-added interferograms for each pixel were Fouriertransformed to yield spectral vectors (or spectral pixels), each with arange of 4000-700 cm⁻¹ at 2 cm⁻¹ intervals. Background spectra for all16 detector elements were collected using 128 co-added interferograms.Raw datasets consist of 409,600 spectra, and occupy about 2.54 GByteseach. This method of collecting spatial data in the form ofinteferograms and then Fourier transforming the interferograms toproduce spectral pixels is well known and is described for example inGriffiths & de Haseth, Fourier Transform Infrared Spectrometry, Elving,Weinefordner & Kolthoff (eds.), John Wiley & Sons, New York (1986). Asan example, each interferogram can contain 8,000 data points and cancorrespond to a pixel sized region of the sample. A one dimensionalFourier transform can then be applied to each interforgram to generate aspectral pixel, each such spectral pixel containing for example 1,600intensity measurements, each of the intensity measurements representingintensity at a particular wavenumber.

It will be appreciated though that the method of reconstructing cellularspectra disclosed herein may also be used with spectral pixel data thatis collected by other means, e.g., without an interferometer and by forexample tuning a monochromatic infrared laser or a tunable filter.

Image Processing

Reconstructed cellular spectra of the cells were then generated usingthe method disclosed above in connection with FIG. 2. In particular, rawdata sets from the infrared micro-spectrometers were imported intosoftware referred to as PapMap. This program is written in 64-bit MATLAB[The Mathworks, Natick, Mass. USA] in order to accommodate the largedata matrices. PapMap reconstructs the spectra of individual cells,collected in mapping mode, from between 9 and 100 individual pixelspectra for each cell. It does so by establishing which pixel spectrabelong to a given cell of the image map. This is accomplished byconstructing a binary mask in which contiguous regions belonging toindividual cells are identified. This mask is established by defining athreshold for the amide I intensity.

For each contiguous area occupied by a cell, the cellular spectrum iscalculated, starting from the spectrum with the largest amide Iintensity. This spectrum is presumably from the nucleus of the cell,which always exhibits the strongest protein intensity.

Once the binary mask associates spectra with their cells, all spectraare subsequently co-added and, subject to several constraints to ensurespectral quality. These criteria are imposed to prevent the co-additionof very weak spectra with poor signal-to-noise to contaminate the cellspectrum, such as spectra from the edges of a cell, which may becontaminated by dispersion artifact.

The co-added cellular spectra, as well as the coordinates of each cell,are then exported for further data analysis. After infrared datacollection, the cells on a slide are stained using standard methods,developed by Papanicolaou, and cover-slipped for cytological follow-up.

Results and Discussion

An example of the potential for using reconstructed cellular spectragenerated according to the method discussed above in connection withFIG. 2 to accurately and reproducibly detect diseased cells at a varietyof progressive states, i.e., Spectral Cytopathology or SCP, is presentedin FIG. 10. In FIG. 10, the diseased cells are compared to controlgroups of similar origin in the oral mucosa to ensure that the spectralchanges are contributed solely by disease rather than origin. Thesensitivity of SCP is seen dramatically seen in FIG. 10A. Here, spectraldata from the palate cells of two patients diagnosed with “reactivechanges” and of one patient diagnosed with squamous cell carcinoma areplotted against spectral data from the normal palate cells of sixvolunteers. The two patients diagnosed with reactive changes also have amedical history of squamous cell carcinoma of the oral mucosa, so theirreactive diagnosis is one deferred as their cells have some residualeffects from a previous or transitioning malignancy. Though the majorityof cells from the three medical samples appear morphologically normal(FIG. 10D), there is some compositional variation shared among them,which deviates from the biochemistry of normal cells (FIG. 10A). Theentirety of two reactive samples cluster completely with the majority ofthe cancer sample (FIG. 10A). This result is expected, as the majorityof most cancer samples contain reactive cells of non-cancerousmorphology, while cells of cancerous morphology (FIGS. 10E and 10G)often make up the minority of samples. In fact, as few as one to threecells of cancerous morphology may be observed in a pre-malignant biopsyand they would be sufficient for a pathological diagnosis. An earlycancer diagnosis, therefore, rests on the detection of few cells in athousand, and if not detected will mean the difference between a normaland malignant diagnosis, despite the number of reactive cells.

By use of SCP, reactive cells can be analyzed, for the first time, andcompared to cancerous cells for the purpose of diagnosis. Reactive cellsreproducibly produce spectral patterns similar to those of diagnosedcancer samples, inferring some malignancy associated transformations.Reactive cells cluster separately from the normal cells, but togetherwith morphologically normal cells from a cancer patient, due to aphenomenon known as “malignancy associated changes” (MACs), which can bedefined as nuclear differences in normal-appearing cells from patientswith present or previous carcinomas. A significant potential of SCP maybe in its sensitivity to detect MACs which can correlate tocompositional states initiated by pre-cancerous states. Interpretationsof a biopsy no longer needs to be made on the behalf of few high-gradecells which may or may not have been prepared on the pathological slide.Instead, the sensitivity of SCP allows for pathological interpretationsto be accurately and reproducibly made throughout the entire biopsy.

The ellipse drawn in FIG. 10A highlights the cells of cancerousmorphology that can be diagnosed by current methods of pathology. Thesefew cells, an example of one shown in FIG. 10E, cluster tightly andfurthest away from the normal cells, registering the largestcompositional variation from normal biochemistry. The implementation ofSCP has blindly distinguished cells by their progression states ofdisease and accurately detected the minority of cells with cancerousmorphology.

FIG. 10B shows a PCA plot of two samples of patients diagnosed withtongue cancer and four samples of normal tongue cells. Only a smallnumber of cells (red squares) from the two cancerous samples can bediagnosed as cancer by current methods of cytology. In contrast, SCPfinds intrinsic compositional changes which significantly vary from thenormal composition of typical tongue cells (FIG. 10B). Though most ofthe sample is comprised of disaggregated cells (FIG. 10F) void of themorphological characteristics common to high grade cancerous cells (FIG.10G), the entire sample produces spectral patterns contributed bydisease state (FIG. 3B). The asterisks, representative of cells from thecancerous samples that are not diagnosable by standard pathology, havesome biochemical changes reproducible in the spectra, which SCP issensitive enough to detect. Again, the compositional changes seen in theasterisks may be a result of MACs. FIG. 10B shows the successfuldetection of cells transitioning from normal state to reactive orpre-cancerous state, and continuing to low grade and high grades ofcarcinoma of the tongue. Results here are correlated to those in FIG.10A of the palate.

FIG. 10C depicts a stack plot of the averaged second derivate,normalized spectra representative of samples in states ranging fromnormal to disease. There is a significant inverse trend in intensitiesof the Amide I and phosphate bands (the vibrations of the phosphodiestergroup, —O—(PO₂)⁻—O—, at 1080 and 1230 cm⁻¹, are referred to as the“phosphate bands”, in accordance with general biochemical nomenclature).As disease progresses, the Amide I decreases in intensity as thephosphate bands increase. This Amide I trend may be associated with thedegradation of common proteins and the expression of different proteinsas cells respond to the disease. Conversely, phosphate band intensitiesincrease as cancerous cells have increased rates of replication. Inaddition, the formation of new proteins as disease progresses isindicated by a low frequency shoulder of the Amide I band at 1618 cm⁻¹,which is reproducible in spectra of diseased cells. Furthermore, theaverage second derivate, normalized spectrum of reactive cells and thatof cancerous cells of normal morphology are virtually identical,supporting SCP's potential for detecting malignancy associated changesthroughout the entire biopsy.

The reconstructed cellular spectra shown in FIG. 10C are slightlydifferent than spectra shown in other drawings herein. Specifically, thespectra shown in FIG. 10C are the second derivative of intensity withrespect to wavenumber (i.e., d²I/dν², where I represents intensity, orabsorbance, of the reconstructed spectra and where ν representswavenumber).

Example 5

FIG. 11 shows another example of how reconstructed cellular spectragenerated according to the method disclosed herein can be used todiscriminate between different types of cells. Panel A of FIG. 11 showsa squamous epithelial cell of the urethra. Panel B of FIG. 11 shows aurothelial epithelial cell of the bladder. Panel C of FIG. 11 shows the2nd derivative with respect to wavenumber of the reconstructed spectrafor the cell shown in panel A. Similarly, panel D of FIG. 11 shows the2^(nd) derivative with respect to wavenumber of the reconstructedspectra of the cell shown in panel B. Panel E shows the PCA scores plotof multiple cells of the types shown in panels A and B, the scores forurethra cells being shown as black circles and the scores for bladdercells being shown as gray stars. As shown, the two types of cells fordistinct clusters in the plot shown in panel E, with the urethra cellsbeing readily distinguishable from the bladder cells.

EQUIVALENTS

The spectral cyto-pathological method of the present invention and manyof its attendant advantages will be understood from the foregoingdescription and it will be apparent that various changes may be madewithout departing from the spirit and scope of the invention orsacrificing all of its material advantages, the form hereinbeforedescribed being merely an exemplary embodiment thereof.

1. A method of generating a spectrum of a cell, the method comprising:(a) receiving a plurality of spectral pixels, each of the spectralpixels corresponding to a portion of the cell, each of the spectralpixels being associated with a plurality of measurements, each of themeasurements being associated with an intensity of light at a particularwavenumber, one of the measurements associated with each spectral pixelbeing a sorting measurement, the sorting measurement being associatedwith a wavenumber within a band of wavenumbers; (b) identifying a subsetof the plurality of the spectral pixels, a first pixel being in thesubset, the sorting measurement of the first pixel being greater than orequal to the sorting measurements of the other spectral pixels, otherpixels in the plurality of spectral pixels being in the subset if theysatisfy a first criteria, a spectral pixel satisfying the first criteriaif that spectral pixel's sorting measurement is greater than a firstthreshold; (c) generating the spectrum, the spectrum having a pluralityof reconstructed measurements, each of the reconstructed measurementscorresponding to a particular wavenumber, each of the reconstructedmeasurements being formed according to a sum of the measurementsassociated with a particular wavenumber of all the pixels in the subset.2. A method according to claim 1, the first threshold being apreselected percentage of the first pixel's sorting measurement.
 3. Amethod according to claim 2, the band of wavenumbers having a lower endand an upper end, the lower and upper ends being user selectable values.4. A method according to claim 3, the lower end being 1640 cm⁻¹ and theupper end being 1670 cm⁻¹.
 5. A method according to claim 3, the sortingmeasurement for each spectral pixel being a peak value of that spectralpixel's associated measurements, the peak value being a peak that isclosest to a user selectable wavenumber.
 6. A method according to claim5, the user selectable wavenumber being 1650 cm⁻¹.
 7. A method accordingto claim 5, pixels in the plurality of spectral pixels being in thesubset only if they satisfy both the first criteria and a secondcriteria, a pixel satisfying the second criteria if a difference betweenthe wavenumber associated with the second pixel's sorting measurementand the wavenumber associated with the first pixel's sorting measurementis less than a second threshold.
 8. A method according to claim 7, thesecond threshold being a user selectable number.
 9. A method accordingto claim 8, the user selectable number being 4 cm⁻¹.
 10. A methodaccording to claim 1, the measurements associated with each spectralpixel representing values derived from light intensity measurements. 11.A method of analyzing the physiological state of a test cell, the methodcomprising: (a) generating a spectrum of the test cell, the methodcomprising: (i) receiving a plurality of spectral pixels, each of thespectral pixels corresponding to a portion of the cell, each of thespectral pixels being associated with a plurality of measurements, eachof the measurements being associated with an intensity of light at aparticular wavenumber, one of the measurements associated with eachspectral pixel being a sorting measurement, the sorting measurementbeing associated with a wavenumber within a band of wavenumbers; (ii)identifying a subset of the plurality of the spectral pixels, a firstpixel being in the subset, the sorting measurement of the first pixelbeing greater than or equal to the sorting measurements of the otherspectral pixels, other pixels in the plurality of spectral pixels beingin the subset if they satisfy a first criteria, a spectral pixelsatisfying the first criteria if that spectral pixel's sortingmeasurement is greater than a first threshold; and (iii) generating thespectrum, the spectrum having a plurality of reconstructed measurements,each of the reconstructed measurements corresponding to a particularwavenumber, each of the reconstructed measurements being formedaccording to a sum of the measurements associated with a particularwavenumber of all the pixels in the subset. (b) determining whether thereconstructed spectrum of the test call has a predetermined criterion,the predetermined criterion being indicative of the physiological stateof the test cell.
 12. The method of claim 11, wherein the predeterminedcriterion is generated from abnormal control epithelial cell spectra orfrom normal control epithelial cell spectra.
 13. The method of claim 11,wherein the epithelial cells in the test and control samples areendothelial, mesothelial or urothelial cells.
 14. A method of detectingan epithelial cell disorder in a test cell, the method comprising: (a)generating a spectrum of a test cell, the method comprising: (i)receiving a plurality of spectral pixels, each of the spectral pixelscorresponding to a portion of the cell, each of the spectral pixelsbeing associated with a plurality of measurements, each of themeasurements being associated with an intensity of light at a particularwavenumber, one of the measurements associated with each spectral pixelbeing a sorting measurement, the sorting measurement being associatedwith a wavenumber within a band of wavenumbers; (ii) identifying asubset of the plurality of the spectral pixels, a first pixel being inthe subset, the sorting measurement of the first pixel being greaterthan or equal to the sorting measurements of the other spectral pixels,other pixels in the plurality of spectral pixels being in the subset ifthey satisfy a first criteria, a spectral pixel satisfying the firstcriteria if that spectral pixel's sorting measurement is greater than afirst threshold; (iii) generating the spectrum, the spectrum having aplurality of reconstructed measurements, each of the reconstructedmeasurements corresponding to a particular wavenumber, each of thereconstructed measurements being formed according to a sum of themeasurements associated with a particular wavenumber of all the pixelsin the subset. (b) determining whether the generated spectrum of thetest cell has a predetermined criterion, the predetermined criterionbeing indicative of the presence of a disorder in the test cell.
 15. Themethod of claim 14, wherein the predetermined criterion is generatedfrom abnormal control epithelial cell spectra.
 16. The method of claim14, wherein the epithelial cells in the test and control samples areendothelial, mesothelial or urothelial cells.
 17. The method of claim14, wherein the epithelial cell disorder is a benign disorder, a viraldisorder, pre-cancer or cancer.
 18. A method analyzing a cell in asample, the method comprising: (a) generating a spectrum of a test cell,the method comprising: (i) receiving a plurality of spectral pixels,each of the spectral pixels corresponding to a portion of the cell, eachof the spectral pixels being associated with a plurality ofmeasurements, each of the measurements being associated with anintensity of light at a particular wavenumber, one of the measurementsassociated with each spectral pixel being a sorting measurement, thesorting measurement being associated with a wavenumber within a band ofwavenumbers; (ii) identifying a subset of the plurality of the spectralpixels, a first pixel being in the subset, the sorting measurement ofthe first pixel being greater than or equal to the sorting measurementsof the other spectral pixels, other pixels in the plurality of spectralpixels being in the subset if they satisfy a first criteria, a spectralpixel satisfying the first criteria if that spectral pixel's sortingmeasurement is greater than a first threshold; (iii) generating thespectrum, the spectrum having a plurality of reconstructed measurements,each of the reconstructed measurements corresponding to a particularwavenumber, each of the reconstructed measurements being formedaccording to a sum of the measurements associated with a particularwavenumber of all the pixels in the subset. (b) determining whether thegenerated spectrum of the test cell has a predetermined criterion, thepredetermined criterion being indicative of the presence of a disorderin the test cell; and (c) forming a reconstructed cellular spectrum, thereconstructed cellular spectrum having a plurality of reconstructedintensities, each of the reconstructed intensities corresponding to aparticular wavenumber, each of the reconstructed intensities beingformed according to a sum of the intensity measurements at a particularwavenumber of the pixels in the subset.